Many methods for detection of target nucleic acids (e.g., SNP genotyping) are known. Currently available homogeneous assays for SNP genotyping include the TAQMAN®, AMPLIFLUOR®, dye binding, allele-selective kinetic PCR, and SCORPION® primer assays. These assays provide one, or at maximum two (if using four different fluorescent dyes) SNPs per reaction well (e.g. dye-binding kinetic PCR requires two wells for one SNP). The available methods for SNP genotyping range from those that allow genotyping of a single SNP in a reaction well to methods that permit genotyping of many thousand SNPs in a single well (e.g., GOLDEN GATE® Assay, Illumina). Present genotyping assay procedures are not readily multiplexed due to the requirement for a different dye for each typed allele, and thus is limited in its potential for improvement. The GOLDEN GATE® assay requires complex analysis devices such as fiber optic array readers. Analyzers for reading of SNP genotyping range from plate readers (optionally, with an included PCR machine), to sequencers (e.g., capillary sequencers), array readers and mass spectrometers. Moreover, to the extent that mass spectrometers have been used for genotyping, currently available procedures do not allow for true multiplexing.